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Running universalizer like this works as expected:
$ universalizer run local_graph/ --update_categories --contexts obo
But omit the contexts argument and it tries to use the default contexts, failing in the process:
$ universalizer run local_graph/ --update_categories
Input path: local_graph/
Will update categories.
Found these graph files:['local_graph/merged-kg_nodes.tsv', 'local_graph/merged-kg_edges.tsv']
Traceback (most recent call last):
File "/home/harry/.cache/pypoetry/virtualenvs/universalizer-fyE8bHoK-py3.9/bin/universalizer", line 5, in <module>
cli()
File "/home/harry/.cache/pypoetry/virtualenvs/universalizer-fyE8bHoK-py3.9/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
return self.main(*args, **kwargs)
File "/home/harry/.cache/pypoetry/virtualenvs/universalizer-fyE8bHoK-py3.9/lib/python3.9/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/home/harry/.cache/pypoetry/virtualenvs/universalizer-fyE8bHoK-py3.9/lib/python3.9/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/harry/.cache/pypoetry/virtualenvs/universalizer-fyE8bHoK-py3.9/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/harry/.cache/pypoetry/virtualenvs/universalizer-fyE8bHoK-py3.9/lib/python3.9/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/home/harry/universalizer/universalizer/cli.py", line 74, in run
if clean_and_normalize_graph(
File "/home/harry/universalizer/universalizer/norm.py", line 85, in clean_and_normalize_graph
remap_these_nodes = make_id_maps(nodepath, os.path.dirname(nodepath), contexts)
File "/home/harry/universalizer/universalizer/norm.py", line 192, in make_id_maps
curie_contexts = load_multi_context(contexts)
File "/home/harry/.cache/pypoetry/virtualenvs/universalizer-fyE8bHoK-py3.9/lib/python3.9/site-packages/prefixmaps/io/parser.py", line 37, in load_multi_context
ctxt.combine(load_context(n, refresh=refresh))
File "/home/harry/.cache/pypoetry/virtualenvs/universalizer-fyE8bHoK-py3.9/lib/python3.9/site-packages/prefixmaps/io/parser.py", line 54, in load_context
with open(data_path / f"{name}.csv", encoding="utf-8") as file:
FileNotFoundError: [Errno 2] No such file or directory: "/home/harry/.cache/pypoetry/virtualenvs/universalizer-fyE8bHoK-py3.9/lib/python3.9/site-packages/prefixmaps/data/['obo',.csv"
The context names appear to be parsed incorrectly.
It's also not possible to pass multiple space-delimited contexts:
$ universalizer run local_graph/ --update_categories --contexts obo bioregistry.upper
Usage: universalizer run [OPTIONS] INPUT_PATH
Try 'universalizer run --help' for help.
Error: Got unexpected extra argument (bioregistry.upper)
This works if they're placed in quotes, which is fine, but that should be in the documentation.
The text was updated successfully, but these errors were encountered:
Running universalizer like this works as expected:
But omit the
contexts
argument and it tries to use the default contexts, failing in the process:The context names appear to be parsed incorrectly.
It's also not possible to pass multiple space-delimited contexts:
This works if they're placed in quotes, which is fine, but that should be in the documentation.
The text was updated successfully, but these errors were encountered: